Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Ubiquitin-NEDD8-like protein RUB1

Gene

RUB1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).By similarity
NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier. An AMP-RUB1 intermediate is formed by an activating enzyme, distinct from the ubiquitin activating enzyme E1, which is composed of a heterodimer AXR1/ECR1. Auxin response is mediated, at least in part, through modification of the cullin AtCUL1 by the attachment of RUB1 to 'Lys-692'.2 Publications

GO - Biological processi

  • ethylene biosynthetic process Source: TAIR
  • protein neddylation Source: TAIR
  • response to auxin Source: TAIR
Complete GO annotation...

Keywords - Biological processi

Ubl conjugation pathway

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-NEDD8-like protein RUB1
Cleaved into the following 2 chains:
Alternative name(s):
Ubiquitin-related protein 1
Short name:
AtRUB1
Gene namesi
Name:RUB1
Synonyms:NEDD8, UBQ15
Ordered Locus Names:At1g31340
ORF Names:T19E23.13
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G31340.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

  • cytosol Source: TAIR
  • nucleus Source: UniProtKB-SubCell
  • plasma membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396910Add
BLAST
Chaini77 – 15276NEDD8-like protein RUB1PRO_0000035965Add
BLAST
Propeptidei153 – 1564CuratedPRO_0000035966

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation
Cross-linki152 – 152Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ9SHE7.
PRIDEiQ9SHE7.

Expressioni

Tissue specificityi

Expressed in leaves, stems and flowers.1 Publication

Interactioni

Subunit structurei

NEDD8-like protein RUB1: Forms a thiol ester with the heterodimer AXR1/ECR1, specifically with the 'Cys-215' of ECR1.

Protein-protein interaction databases

BioGridi25258. 3 interactions.

Structurei

Secondary structure

1
156
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi78 – 825Combined sources
Beta strandi88 – 925Combined sources
Helixi99 – 11012Combined sources
Helixi114 – 1163Combined sources
Beta strandi117 – 1215Combined sources
Helixi133 – 1353Combined sources
Beta strandi142 – 1476Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BT0X-ray1.70A77-152[»]
ProteinModelPortaliQ9SHE7.
SMRiQ9SHE7. Positions 1-152.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9SHE7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-like 1PROSITE-ProRule annotationAdd
BLAST
Domaini77 – 15276Ubiquitin-like 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ubiquitin family.Curated
Contains 2 ubiquitin-like domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG5272.
InParanoidiQ9SHE7.
KOiK12158.
OMAiINIEPND.
PhylomeDBiQ9SHE7.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamiPF00240. ubiquitin. 2 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 2 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 2 hits.
PROSITEiPS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9SHE7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLADYN IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDTID
110 120 130 140 150
RIKERVEEKE GIPPVQQRLI YAGKQLADDK TAKDYNIEGG SVLHLVLALR

GGFGLL
Length:156
Mass (Da):17,397
Last modified:August 10, 2010 - v3
Checksum:iFA8D702BB9C1B3AE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007654 Genomic DNA. Translation: AAF24594.1.
CP002684 Genomic DNA. Translation: AEE31344.1.
BT005749 mRNA. Translation: AAO64156.1.
BT006110 mRNA. Translation: AAP04095.1.
AK228591 mRNA. Translation: BAF00506.1.
PIRiC86439.
RefSeqiNP_564379.2. NM_102873.4.
UniGeneiAt.25337.
At.30783.
At.43046.

Genome annotation databases

EnsemblPlantsiAT1G31340.1; AT1G31340.1; AT1G31340.
GeneIDi840023.
KEGGiath:AT1G31340.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007654 Genomic DNA. Translation: AAF24594.1.
CP002684 Genomic DNA. Translation: AEE31344.1.
BT005749 mRNA. Translation: AAO64156.1.
BT006110 mRNA. Translation: AAP04095.1.
AK228591 mRNA. Translation: BAF00506.1.
PIRiC86439.
RefSeqiNP_564379.2. NM_102873.4.
UniGeneiAt.25337.
At.30783.
At.43046.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BT0X-ray1.70A77-152[»]
ProteinModelPortaliQ9SHE7.
SMRiQ9SHE7. Positions 1-152.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi25258. 3 interactions.

Proteomic databases

PaxDbiQ9SHE7.
PRIDEiQ9SHE7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G31340.1; AT1G31340.1; AT1G31340.
GeneIDi840023.
KEGGiath:AT1G31340.

Organism-specific databases

TAIRiAT1G31340.

Phylogenomic databases

eggNOGiCOG5272.
InParanoidiQ9SHE7.
KOiK12158.
OMAiINIEPND.
PhylomeDBiQ9SHE7.

Miscellaneous databases

EvolutionaryTraceiQ9SHE7.
PROiQ9SHE7.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamiPF00240. ubiquitin. 2 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 2 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 2 hits.
PROSITEiPS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "The ubiquitin-related protein RUB1 and auxin response in Arabidopsis."
    del Pozo J.C., Timpte C., Tan S., Callis J., Estelle M.
    Science 280:1760-1763(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH AXR1 AND ECR1.
  6. "The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1."
    del Pozo J.C., Estelle M.
    Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
    Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
    Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-29; LYS-33; LYS-48 AND LYS-63.
    Strain: cv. Landsberg erecta.
  8. "The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis."
    Rao-Naik C., delaCruz W., Laplaza J.M., Tan S., Callis J., Fisher A.J.
    J. Biol. Chem. 273:34976-34982(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 79-152, TISSUE SPECIFICITY.

Entry informationi

Entry nameiRUB1_ARATH
AccessioniPrimary (citable) accession number: Q9SHE7
Secondary accession number(s): O80715
, P59263, Q0WQU3, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2003
Last sequence update: August 10, 2010
Last modified: June 24, 2015
This is version 108 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.